With vSphere 6.0, You will be able to backup your virtual machines. FT supports for vStorage APIs for Data Protection (VADP) and it also supports all leading VADP solutions in Market like symantec, EMC, HP ,etc.

New version of FT keeps the Separate copies of VM files like .VMX, .VMDk files to protect primary VM from both Host and Storage failures. You are allowed to keep both Primary and Secondary VM files on different datastore